Cross-references to external classification systems
Gene Ontology terms are mapped to commonly used bioinformatics resources whenver possible. These mappings (or “cross-references”) create a network of information that integrate GO and its annotations with other biological databases and resources.
External classification systems mapped to GO terms:
| Database resource | Scope | Relevant GO aspect(s) | Direct access to mapping file(s) |
|---|---|---|---|
| Enzyme Commission (EC) | Catalytic reactions | Molecular Function | ec2go |
| KEGG: Kyoto Encyclopaedia of Genes and Genomes | Catalytic reactions | Molecular Function | kegg_reaction2go |
| HAMAP | High-Quality Automated and Manual Annotation of Microbial Proteomes | All aspects | hamap2go |
| InterPro | Protein families, domains and functional sites. Ecnompasses contributing databases: PantherDB, PFAM, PIRSF, [PRINTS], PROSITE and SMART | All aspects | interpro2go |
| MetaCyc | Biological pathways and catalytic reactions | Molecular Function & Biological Process | metacyc2go |
| Reactome | Events and catalyst activities | Molecular Function | reactome2go |
| Rfam - RNA families |
RNA entities | All aspects | rfam2go |
| Rhea | Catalytic reactions | Molecular Function | rhea2go |
| UM-BBD | Biocatalysis/Biodegradation Database: enzymes, reactions and pathways | Molecular Function & Biological Process | um-bbd_enzymeid2go um-bbd_reactionid2go um-bbd_pathwayid2go |
| UniProt Keywords | Mapping of GO terms to UniProt Knowledgebase keywords. | All aspects | uniprotkb_kw2go |
| UniProt Subcellular location | UniProt Subcellular location terms | Cellular Component | uniprotkb_sl2go |
| UniRules | UniProt Automatic Annotation pipeline | All aspects | unirule2go |
| Wikipedia | General | All aspects | wikipedia2go |
Direct access to the mappings file directory: https://current.geneontology.org/ontology/external2go/.
Cross-references files format
-
Header describing the date generated and the GO release used, for example:
! Generated on 2018-10-05T08:40Z from the ontology 'go' with data version: 'releases/YYYY-MM-DD' -
Each cross-reference is on a different line, in the format:
database:term identifier (id/name) > GO:GO term name ; GO:idFor example:
EC:1.1.1.1 > GO:alcohol dehydrogenase (NAD+) activity ; GO:0004022
Mapping types & cardinality
- The cardinality of some of cross-references can be many-to-many; others are restricted.
- Cross-references can be one of 4 types: exact, broad, narrow general database cross references
- Exact database cross references: GO and cross reference object have the same meaning.
- Cardinality: 1:1
- Narrow database cross references: The concept represented by the cross-reference represents a narrower or more specific concept than the GO term.
- Cardinality: 1 GO:n narrow cross-references
- Broad database cross references: The concept represented by the cross-reference represents a broader or more general concept than the GO term.
- Cardinality: n:n
- Related database cross references: The concept represented by the cross-reference is broad in some aspect, narrow in another.
- Cardinality: n:n
- Exact database cross references: GO and cross reference object have the same meaning.
- Cross references deprecated in the source database should not be included in GO.
Using and citing cross-references and mappings
If you have used a mapping in a publication or presentation, please ensure that you cite both the GO knowledgebase and the source of the mapping. See the GO citation guide for citing the GO knowledgebase.